Page History

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• wget – retrieves the contents of an Internet URL
• cp – copies files located on any local file system
• scp – copies files to/from a remote system
• rsync – copies directories or files on either local or remote systems

Local file systems

There are 3 local file systems available on any TACC compute cluster (Lonestar5stampede2, stampede2 lonestar5, etc.), each with different characteristics. All these local file systems are very fast and set up for parallel I/O (Lustre file system).

On ls5 stampede2 these local file systems have the following characteristics:

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--------------------- Project balances for user abattenh ----------------------
| Name           Avail SUs     Expires  | Name           Avail SUs     Expires |
| CancerGeneticsgenomeAnalysis       4856673  20182021-0903-3031 | A-cm10BioinformaticsResour 100             1096  2018-12-312020-06-30 |
| UT-2015-05-18       21001000  20192021-03-31 | DNAdenovo  genomeAnalysis      2500  2019-03 4969  2021-03-31 |
| CancerGenetics      4856  2020-09-30 | A-cm10              8867  2020-12-31 |
------------------------ Disk quotas for user abattenh -------------------------
| Disk         Usage (GB)     Limit    %Used   File Usage       Limit   %Used |
| /home1              0.0      10.0     0.1210           91153     1000000    0.0102 |
| /workwork2             538614.5    1024.0    5260.5901        6105361094     3000000    2.04 |
| /scratch         37252676.96       0.0     0.00        32442 4137           0    0.00 |
-------------------------------------------------------------------------------

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When you first login, you start in your home directory. Use these the cd, cdw2 and cds commands to change to your other file systems. Notice how your command prompt helpfully changes to show your location.

cdwcdw2
cds
cd

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TACC compute clusters now share a common Work file system called stockyard. So files in your Work area do not have to be copied, for example from ls5 to stampede2 to ls5 – they can be accessed directly from either cluster.

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• $STOCKYARD - This refers to the root of your shared Work area
  • e.g. /work/01063/abattenh  (should be changed to /work2/01063/abattenh soon)
    
• $WORK or $WORK2 - Refers to a sub-directory of the shared Work area that is different for different clusters, e.g.:
  
  • /work/01063/abattenh/lonestar on ls5
  • /workwork2/01063/abattenh/stampede2 on stampede2

A mechanism for purchasing larger stockyard allocations (above the 1 TB basic quota) from TACC are in development.

The UT Austin BioInformatics Team, a loose group of bioinformatics researchers, maintains a common directory area on stockyard.

ls /workwork2/projects/BioITeam

Files we will use in this course are in a sub-directory there:. The $CORENGS environment variable set in your login profile refers to this path.

echo $CORENGS
ls /workwork2/projects/BioITeam/projects/courses/Core_NGS_Tools

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corral is a gigantic (multiple PB) storage system (spinning disk) where researchers can store data. UT researchers may request up to 5 TB of corral storage through the normal TACC allocation request process. Additional space on corral can be rented for ~$85~$80/TB/year.The UT/Austin BioInformatics Team also has an older, common directory area on corral.

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ls /corral-repl/utexas/BioITeam

A couple of things to keep in mind regarding corral:

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ranch is a gigantic (multiple PB) tape archive system where researchers can archive data. All TACC users have an automatice 2 TB ranch allocation. UT researchers may request large larger (multi-TB) ranch storage allocations through the normal TACC allocation request process.

There is currently no charge for ranch storage. However, since the data is stored on tape it is not immediately available – robots find and mount appropriate tapes when the data is requested, and it can take minutes to hours for the data to appear on disk. ( The metadata about your data – the directory structures and file names – is always accessible, but the actual data in the files is not on disk until "staged". See the ranch user guide for more information: https://www.tacc.utexas.edu/user-services/user-guides/ranch-user-guide.

Once that data is staged to the ranch disk it can be copied to other places. However, the ranch file system is not mounted as a local file system from the stampede2 or ls5 clusters. So remote copy commands are always needed to copy data to and from ranch (e.g. scp, rsync).

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The first task is to get this sequencing data to a permanent storage area. This should not be your laptop or one of the TACC local file systems! corral ! corral (or stockyard) is a great place for it, or a server maintained by your lab or company.We'

re going to pretend – just for the sake of this class – that Here's an example of a "best practice". Wherever your permanent storage area is in your TACC work area. Execute these commands to make your "archive" directory and some sub-directories.

mkdir -p $WORK/archive/original/2018_05.core_ngs

Here's an example of a "best practice". Wherever your permanent storage area is, it should have a rational sub-directory structure that reflects its contents. It's easy to process a few NGS datasets, but when they start multiplying like tribbles, good organization and naming conventions will be the only thing standing between you and utter chaos!

For example:

, it should have a rational sub-directory structure that reflects its contents. It's easy to process a few NGS datasets, but when they start multiplying like tribbles, good organization and naming conventions will be the only thing standing between you and utter chaos!

For example:

• original – for original sequencing data (compressed FASTQ files)
  • sub-directories named, for example, by year_month.<project_name>
• aligned – for alignment artifacts (BAM files, etc)
  • sub-directories named, e.g., 
  original – for original sequencing data (compressed FASTQ files)
  • sub-directories named, for example, by year_month.<project_name>
• aligned – for alignment artifacts (BAM files, etc)
  • sub-directories named, e.g.,  by year_month.<project_name>
• analysis – further downstream analysis
  analysis – further downstream analysis
  • reasonably named sub-directories, often by project
  • genome refs – reference genomes and other annotation files used in alignment and analysis
    
    • sub-directories for different reference genomes
    • e.g. ucsc/hg19, ucsc/sacCer3, mirbase/v20
  • code – for scripts and programs you and others in your organization write
    • ideally maintained in a version control system such as git, subversion or cvs.
    • easiest to name sub-directories for people.

  ...

  Get ready to run wget from the directory where you want to put the data.

  Don't press Enter after the wget command – just put a space after it.

  Code Block
  language bash title Get ready to wget
  mkdir -p $SCRATCH/archive/original/2021.core_ngs cd $WORK$SCRATCH/archive/original/2018_052021.core_ngs wget

  Here are two web links:

  • httphttps://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gzhttp
  • https://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R2.cat.fastq.gz

  Right-click (Windows) or Control+click (Mac) on the 1st link in your browser, then select "Copy link location" from the menu. Now go back to your Terminal. Put your cursor after the space following the wget command then either right-click (Windows), or Paste (Command-V on Mac, Control-V on Windows). The command line to be executed should now look like this:

  Code Block
  language bash title wget to retrieve a web URL
  wget http://web.corral.tacc.utexas.edu/BioITeamBioinformaticsResource/CoreNGS/yeast_stuff/Sample_Yeast_L005_R1.cat.fastq.gz

  Now press Enter to get the command going. Repeat for the 2nd link. Check that you now see the two files (ls).

  Copy from a corral location - cp or rsync

  Suppose you have a corral allocation where your organization keeps its data, and that the sequencing data has been downloaded there. You can use various Linux commands to copy the data locally from there to your $SCRATCH area.

  cp

  The cp command copies one or more files from a local source to a local destination. It has the most common form:

  cp [options] <source file 1> <source file 2> ... <destination directory>/

  Make a directory in your scratch area and copy a single file to it. The trailing slash ( / ) on the destination says it is a directory.

  Tip
  By default wget creates a file in the current directory matching the last component of the URL (e.g. Sample_Yeast_L005_R1.cat.fastq.gz here). You can change the copied file name with wget's -O option. Also note that if you execute the same wget more than once, subsequent local files will be named with a .1, .2, etc. suffix.

  Copy from a corral location - cp or rsync

  Suppose you have a corral allocation or stockyard area where your organization keeps its data, and that the sequencing data has been downloaded there. You can use various Linux commands to copy the data locally from there to your $SCRATCH area.

  cp

  The cp command copies one or more files from a local source to a local destination. It has the most common form:

  cp [options] <source file 1> <source file 2> ... <destination directory>/

  Make a directory in your Scratcharea and copy a single file to it. The trailing slash ( / ) on the destination says the destination is a directory.

  Code Block
  language bash title Single file copy with cp
  mkdir -p $SCRATCH/data/test1 cp $CORENGS/
  Code Block
  language bash title Single file copy with cp
  mkdir -p $SCRATCH/data/test1 cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools/misc/small.fq $SCRATCH/data/test1/ ls $SCRATCH/data/test1 # or.. mkdir -p ~/scratch/data/test1 cd ~/scratch/data/test1 cp /work/projects/BioITeam/projects/courses/Core_NGS_Tools $CORENGS/misc/small.fq . ls

  Copy an entire directory to your scratch Scratch area. The -r argument option says "recursive".

  Code Block
  language bash title Directory copy with cp
  mkdir -p $SCRATCH/data cds cd data cp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools$CORENGS/general/ general/

  Exercise: What files were copied over?

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  rsync is a very complicated program, with many options (http://rsync.samba.org/ftp/rsync/rsync.html). However, if you use the recipe shown here for directories, it's hard to go wrong:

  rsync -ptlrvP avW local/path/to/source_directory/ local/path/to/destination_directory/

  Both the source and target directories are local (in some file system accessible directly from ls5 stampede2). Either full or relative path syntax can be used for both. The -ptlrvPavW options above stand for:

  • -a means "archive mode", which implies the following options (and a few others)
    
    • -p
    means
    • – preserve file permissions
    • -t
    means
    • – preserve file times
    • -l
    means
    • – copy symbolic links as links
    • -r
    means recursively copy sub-directories
  • -v means verbose
  • • – recursively copy sub-directories
  • -v means verbose
  • -W means transfer Whole file only
    • Normally the rsync algorithm compares the contents of files that need to be copied and only transfers the different parts.
    • For large files and binary files, figuring out what has changed (diff-ing) can take more time than just copying the whole file.
    • The -W option disables file content comparisons (skips diff-ing)
    -P means show Progress
    • .

  Since these are all single-character options, they can be combined after one option prefix dash ( - ). You could also use options -arvP, where ptlrvW, separately, instead of using -a means for "archive mode", which implies the -ptl options.

  Tip
  title Always add a trailing slash ( / ) after directory names
  The trailing slash ( / ) on the source and destination directories are very important for rsync (and for other Linux copy commands also)! rsync will create the last directory level for you, but earlier levels must already exist.

  Code Block
  language bash title rsync (local directory)
  mkdir -p $SCRATCH/data cds rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_avW $CORENGS/custom_tracks/ data/custom_tracks/

  ...

  Code Block
  language bash
  rsync -ptlrvPavW /work/projects/BioITeam/projects/courses/Core_NGS_Tools/ucsc_custom_tracks/ data/custom_tracks/

  Tip
  The bash shell has several convenient line editing features: use the Up arrow to scroll back through the command line history; Down arrow goes forward use Ctrl-a to move the cursor to the beginning of a line; Ctrl-e to the end use Backspace to remove text before the cursor; Delete to remove text after the cursor use Ctrl-a and then Ctrl-k to delete all text on your command line

  Copy from a remote computer - scp or rsync

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  Copy a single file to your $SCRATCH/data/test1 directory from the server named gapdhdragonfly.icmb.utexas.edu, using the user account corengstools. When prompted for a password, use the one we have written on to the board Zoom chat (or copy/paste the password from this file: $CORENGS/tacc/gapdhdragonfly_access.txt)

  Code Block
  title single remote file copy with scp
  cds cat $CORENGS/tacc/gapdhdragonfly_access.txt cds mkdir -p data/test2 scp corengstools@gapdhcorengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/progeria_ctcf.vcf.gz ./data/test1test2/ ls ./data/test1test2

  Notes:

  • The 1st time you access a new host the SSH security prompt will appear
  • You will be prompted for your remote host password
  • The  -r recursive argument works for scp also, just like for cp

  ...

  • The tilde ( ~ ) at the start of the path means "relative to my home directory"We traverse through the BioITeam symbolic link created in your home directory earlier.
  • We use the same tilde ( ~ ) in the destination to traverse the scratch symbolic link in your home directory.
    

  Don't forget to change userid below.

  • 
    

  Code Block
  language bash title rsync (remote directory)
  rsync -ptlrvPavW corengstools@gapdhcorengstools@dragonfly.icmb.utexas.edu:~/custom_tracks/ ~/scratch/data/custom_tracks/

  ...

  Expand
  title Answer
  No, because all the source files were already present in the destination directory (you copied the same files earlier) with the same timestamps and file checksums. So rsync had nothing to do!

  ...

  Code Block
  title Play a scavenger hunt for more practice
  cd cp -r /workwork2/projects/BioITeam/projects/courses/Core_NGS_ToolsTools/linuxpractice/what what # or using the $CORENGS environment variable cp -r $CORENGS/linuxpractice/what what cd what cat readme

  Where are you when you're all done?

  Expand
  title Answer
  ls5:~/what/starts/here/changes/the/world

  step by step answers

  stamp2:~/what/starts/here/changes/the/world

  step by step answers

  Expand
  title Step 1 answer
  From inside your ~/what directory: Code Block title Play a scavenger hunt for more practice mkdir starts cd starts cp /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/nextInstr . cat nextInst

  Expand
  title Step 2 answer
  From inside your ~/what/starts directory: Code Block title Play a scavenger hunt for more practice mkdir startshere cd startshere cpwget http:/work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/steps/nextInstr . cat nextInst/web.corral.tacc.utexas.edu/BioinformaticsResource/CoreNGS/step3.txt cat step3.txt

  Expand
  title Step 3 answer
  From inside your ~/what/starts/here directory: Code Block title Play a scavenger hunt for more practice mkdir here cd here wget http://web.corral.tacc.utexas.edu/BioITeam/step3.txt cat step3.txt
  Expand
  title Step 4 answer
  From inside your ~/what/starts/here directory: Code Block title Play a scavenger hunt for more practice rsync -ptlrvP /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/ # or scp -r scp -r /work/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes changes scp -r /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/ # or rsync -ptrvP /work2/projects/BioITeam/projects/courses/Core_NGS_Tools/linuxpractice/changes/ changes/ # Note: rsync -avP ... will also work, but will report an error because the destination file and # directory ownership cannot be changed to match the source. But the files will be copied, and # ownership assigned to you.   # Then cd changes more largeFile.txt

  Expand
  title Step 5 4 answer
  From inside your ~/what/starts/here/changes directory: Code Block title Play a scavenger hunt for more practice rsync -avP corengstools@dragonfly.icmb.utexas.edu:~/the/ -ptlrvP corengstools@gapdhthe/ # or scp -r corengstools@dragonfly.icmb.utexas.edu:~/the/ the/ cd the cat instr5.txt cd world cat instr6.txt

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